I've noticed that when I assign partial charges using the charmm27 forcefield for ASP residues, the charges are assigned exactly as listed in the top_al27_prot_na.rtf file.
But if I modify the ASP residue to be neutral the charges seem to be assigned based on the bond increment file (charmm22_templates.inc). This is puzzling since the top_al27_prot_na.rtf file already gives partial charge assignments for a protonated ASP (called ASPP)
So two questions:
1) Why isn't the charges from the ASPP residue template assigned to the protonated ASP?
2) What other amino acids are affected this way? In other words, when does Accelrys use the partial charges in the top_al27_prot_na.rtf file and when does it make up its own charges?
But if I modify the ASP residue to be neutral the charges seem to be assigned based on the bond increment file (charmm22_templates.inc). This is puzzling since the top_al27_prot_na.rtf file already gives partial charge assignments for a protonated ASP (called ASPP)
So two questions:
1) Why isn't the charges from the ASPP residue template assigned to the protonated ASP?
2) What other amino acids are affected this way? In other words, when does Accelrys use the partial charges in the top_al27_prot_na.rtf file and when does it make up its own charges?
